Brain data

Contents

Brain data¶

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Gray matter qMRI¶

Code imports¶

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data¶

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

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Load data plot it¶

dataset.load()

dataset.data_type

'brain'

fig_gm = Plot(dataset, plot_name = 'new-fig-2')

fig_gm.title = 'Brain gray matter qMRI microstructure'

fig_gm.display('jupyter-book', tissue = 'GM')

White matter qMRI¶

fig_wm = Plot(dataset, plot_name = 'new-fig-4')

fig_wm.title = 'Brain white matter qMRI microstructure'

fig_wm.display('jupyter-book', tissue = 'WM')

Spine¶

data_type = 'spine'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

dataset.load()
dataset.data['T1w']

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	Subject	Session	Timestamp	SCT Version	Filename	Slice (I->S)	VertLevel	MEAN(area)	STD(area)	MEAN(angle_AP)	...	STD(diameter_AP)	MEAN(diameter_RL)	STD(diameter_RL)	MEAN(eccentricity)	STD(eccentricity)	MEAN(orientation)	STD(orientation)	MEAN(solidity)	STD(solidity)	SUM(length)
1	1	1	2021-06-09 23:24:10	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	31:75	2:3	67.680431	1.598728	-4.254822	...	0.225578	10.843164	0.307774	0.680936	0.039585	2.149545	1.734302	0.980308	0.009615	36.167347
6	1	2	2021-06-09 23:24:19	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	47:86	2:3	67.511930	1.726861	-6.577358	...	0.186145	10.874612	0.275935	0.690540	0.031751	2.855729	1.967201	0.977647	0.008612	32.528253
0	1	3	2021-06-09 23:24:08	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	51:93	2:3	64.109061	3.127582	-4.670983	...	0.464761	10.640776	0.333651	0.690605	0.054994	3.202127	2.184708	0.976971	0.007494	34.565242
8	2	1	2021-06-09 23:41:15	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	1:38	2:3	66.455289	4.204379	0.095829	...	0.684070	11.992443	0.585042	0.794791	0.061804	2.234122	1.464966	0.963074	0.016533	31.424022
10	2	2	2021-06-09 23:41:24	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	12:50	2:3	73.688109	2.833139	-0.068322	...	0.406465	12.065046	0.492764	0.756302	0.053939	2.367144	1.803792	0.966030	0.009791	32.356730
15	2	3	2021-06-09 23:50:43	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	3:39	2:3	73.905494	2.073274	-0.691532	...	0.368828	12.371408	0.639116	0.780126	0.052688	1.694898	1.187327	0.963111	0.014391	30.534960
12	2	4	2021-06-09 23:41:39	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	9:46	2:3	69.405673	4.568637	-0.749008	...	0.543059	12.227376	0.665839	0.796428	0.053488	2.145301	1.623586	0.958420	0.020529	31.442066
9	3	1	2021-06-09 23:41:20	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	51:85	2:3	59.927681	1.980624	-0.778617	...	0.334499	10.086060	0.232852	0.658816	0.049798	2.475063	1.644264	0.972640	0.009458	28.297791
13	3	2	2021-06-09 23:41:42	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	33:66	2:3	60.228814	1.776652	-1.464265	...	0.247391	10.486967	0.214164	0.716856	0.033921	1.850661	1.538691	0.966100	0.007298	27.236579
11	3	3	2021-06-09 23:41:39	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	43:77	2:3	60.621684	1.733616	-0.009478	...	0.358365	10.632869	0.308162	0.726909	0.049649	1.681134	1.217510	0.970807	0.010769	28.389363
16	3	4	2021-06-09 23:55:17	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	40:74	2:3	59.915665	2.030933	-2.222570	...	0.296578	10.445562	0.243935	0.716104	0.038919	2.551453	2.010580	0.972863	0.010084	28.329492
17	4	2	2021-06-09 23:55:38	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	49:84	2:3	59.717857	2.220913	2.572138	...	0.399145	10.999128	0.354854	0.775108	0.045832	2.195005	1.555832	0.972639	0.015228	29.056988
18	4	3	2021-06-09 23:55:53	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	43:77	2:3	61.969221	2.026699	6.989458	...	0.326731	10.956739	0.419218	0.753243	0.040568	2.095929	1.251544	0.976777	0.009427	28.313078
4	5	1	2021-06-09 23:24:18	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	19:57	2:3	53.010013	11.097434	-1.790824	...	1.087683	10.965275	0.675722	0.822167	0.059414	4.036279	2.295310	0.952220	0.027352	33.355815
14	5	2	2021-06-09 23:41:45	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	44:82	2:3	64.717972	4.153035	-3.034680	...	0.567947	11.448594	0.408139	0.769825	0.056204	4.103625	1.847953	0.966696	0.012619	32.529064
2	6	1	2021-06-09 23:24:11	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	45:81	2:3	62.953114	1.769023	-0.646246	...	0.216321	11.513113	0.470660	0.792890	0.029588	1.260913	1.049494	0.965233	0.014776	30.644730
7	6	2	2021-06-09 23:24:21	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	89:125	2:3	64.823566	18.835219	13.113466	...	1.159209	9.503113	2.506067	0.576338	0.152557	22.042768	32.322329	0.968538	0.032237	10.122137
5	6	3	2021-06-09 23:24:19	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	38:75	2:3	62.990802	2.049191	-2.338349	...	0.298265	11.506661	0.596266	0.792194	0.041279	1.614134	1.158783	0.973527	0.010495	31.364216
3	6	4	2021-06-09 23:24:12	git-jca/3413-run-batch-session-c41958db922273a...	/Users/julien/temp/neuromod/data_processed/sub...	58:95	2:3	63.925810	2.765595	-1.132526	...	0.248317	11.727604	0.490648	0.803257	0.028672	1.754369	1.049329	0.971605	0.012450	31.247426

19 rows × 24 columns

fig_spine = Plot(dataset, plot_name = 'new-fig-2')

fig_spine.title = 'Spinal cord CSA [T<sub>1</sub>w/T<sub>2</sub>w]'

fig_spine.display('jupyter-book', tissue = 'WM')

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